What is MDL Chime?

"Chime" is pronounced like the gong ("Ch" as in chimney), despite its name being derived from Chemical MIME.

MDL Chime is being phased out. Its development largely ceased in 1998 (see version history). MDL has refused to open Chime's source code, thereby precluding further development by the community of biochemists who use it. New work that displays rotatable, interactive molecular views in web browsers is being done largely with the Jmol java applet (See examples here). Jmol is an open source project, and has been very actively developed in recent years (through 2007). Most of the Chime/RasMol command language has been implemented in Jmol. Jmol is now considerably more powerful than Chime, and, being a java applet, needs no installation, and works as well in Mac OSX (Safari) or Linux (Firefox) as it does on MS Windows (Internet Explorer 7 or Firefox).

Nevertheless, MolviZ.Org will continue to offer the existing Chime resources simply because it will take years before most of them can be converted to Jmol.

MDL Chime (or simply "Chime" for short) is a free program to show molecular structure in three dimensions. Its images look like RasMol's because Chime is derived, in part, from RasMol. MDL Chime differs from RasMol in that Chime sits directly on a web page (runs inside your browser as a plug-in), whereas RasMol is a stand-alone program (runs outside your browser, independently). MDL Chime also differs in that most Chime-employing websites show only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file. However, some Chime websites also provide support for showing any molecule of interest, and doing self-directed exploration similar to RasMol, notably Protein Explorer.

MDL Chime's ability to support educational resources has had a large impact on stuctural biochemistry education, as exemplified by the many excellent resources indexed in the World Index of Molecular Visualization Resources.

MDL Chime can be downloaded free from the web site of its corporate creators, MDL. See MDL Chime: Browsers, Platforms, Installation, Troubleshooting. MolViz.Org illustrates what MDL Chime is cabable of, and provides help for developing tutorials and presentations employing MDL Chime. An ongoing discussion of technical issues about Chime may be seen in the history of the RasMol email list.

Monomer of Oxy-hemoglobin zooming in to oxy-heme (from 1HHO by B. Shaanan). This is an animated picture; you cannot move it with your mouse, unlike when actually displayed in MDL Chime.

A Brief History of Chime

Chime (more completely referred to as MDL Chime) was developed largely by Tim Maffett and Bryan van Vliet (while at MDL). Chime incorporates the command processer and rendering engine from RasMol, whose source code was put into the public domain by its author, Roger Sayle. Maffett and van Vliet had the foresight to leave the entire RasMol command processor in Chime, which explains much of its power and popularity with biochemists. (Only RasMol's "save" commands were disabled in Chime. These write files to your disk under the control of command scripts, which can come from websites, posing a security risk. However, Chime's menu can save the currently displayed PDB file to your disk.)

Complete history of Chime versions.

How to Create Chime Tutorials

There are several ways to approach creating a Chime tutorial. Some require little or no technical or programming skills, and others are more demanding. Here are links to several different resources.

Presenting RasMol-Saved Scripts with Chime. No programming required! This example uses Gal4 Transcriptional Regulatory Protein Complexed to DNA. (Gal4 en Español)
Programming Chime Web Pages from Scratch. This tutorial is *Win-IE-Compatible* but requires knowledge of programming.
Tools for Authoring Chime Resources are indexed at the World Index of Molecular Visualization Resources (molvisindex.org).
Chime command language: Reference manuals on script commands and embed tags.
*Win-IE-Compatibility* issues are detailed in Protein Explorer. Go to proteinexplorer.org and click the link to Help/Index/Glossary (on the FrontDoor, right-hand gray box). Click on "I" and look for the entry on Internet Explorer, where you will find links to detailed documents. See also the Molecular Visualization Freeware Email List.
Chime Toolbox at Cabrillo College Computers in Chemistry. Advanced Chime usage and controls. Animated energy diagrams linked to animated chemical reactions, and sliders that control Chime. From Albion Baucom and Harry Ungar at Cabrillo College, Aptos CA US.

Chime Command Language

Reference Manuals: No single manual documents the entire set of Chime commands. Instead, Chime commands are documented in two parts:

The RasMol 2.6 Command Language Reference Manual contains all the RasMol 2.6 commands. All were incorporated into Chime except the "Save" commands, which would have presented a security risk in a browser. This manual does not include the Chime-specific commands, which are documented in the manual immediately below.

The MDL Chime Command Reference Manual contains the rest of the Chime commands. This manual does not include the extensive command set Chime shares with RasMol, which is documented in the manual immediately above. If the above link doesn't work (MDL has changed their website often), go to mdl.com and look for Support, then Developer Support, then Chime.

Additional information about Chime commands:

Select Commands in RasMol and Chime

RasMol/Chime Color RGB Values

Bonds in RasMol/Chime including

What are the values used by RasMol and Chime for van der Waals radii in the spacefill rendering?

How do RasMol and Chime determine which atoms in a PDB file are covalently bonded?

How can arbitrary bonds be added or hidden?

Why don't RasMol or Chime show most of the hydrogen bonds?

Chime Embed Tag Parameters from MDL.Chime is invoked with an HTML embed tag. The embed tag contains parameters that may specify the molecule to be loaded, the initial rendering and color scheme, and other Chime behaviors. Some behaviors of Chime can be controlled only by embed tag parameters. Examples include "debugscript" mode, and "menudelay".

Other Chime support documents and tutorials may be found at MDL Chime Developer Support

Frequently Asked Questions About Chime

Martz's Frequently Asked Questions (FAQ).
MDL's Chime FAQ.
Chime is often discussed on the Molecular Visualization Freeware Email List. Chime is occasionally discussed on the PDB Email List.
Chime vs. RasMol. Chime has enormous advantages over RasMol for educational tutorials. Here are the details.
How Chime Works. Explains the steps that occur when you view a molecule in Chime.
Command Line Interface Example. Developing a Chime tutorial? This example shows how to program your web page to accept commands that control the Chime molecule. Useful for development and for teaching the Chime command language.
Origins of MDL Chime: see History of Visualization of Biological Macromolecules, which incudes the context in which Chime was first created, its relation to RasMol, and its first uses.

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Feedback to Eric Martz.